Non-destructive read operations with dynamically growing images

ABSTRACT

Methods and digital imaging devices disclosed herein are adapted to capture images of a specimen in a chemical reaction using a series of short exposures of light emissions from the specimen over a period of time. The series of short exposures is captured using an array of pixels of an image sensor in the digital imaging device that are configured for performing continuous non-destructive read operations to read out a set of non-destructive read images of the specimen from the pixel array. In one embodiment, images are captured by delaying the read out until at or near the end of the chemical reaction to reduce read noise in the images. The signals read out from the image sensor can be continuously monitored and the capturing of images can be discontinued either automatically or based on a command from a user. The captured images can then be displayed in a graphical display.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a nonprovisional of and claims the benefit ofpriority of U.S. Provisional Application No. 61/915,930, titled,“Non-Destructive Read Operations With Dynamically Growing Images,” filedon Dec. 13, 2013, which is herein incorporated by reference it itsentirety for all purposes.

FIELD OF THE INVENTION

The embodiments described herein relate generally to capturing images ofspecimens in chemical reactions. More particularly, embodiments relateto capturing images of specimens in chemical reactions usingnon-destructive read operations in a digital imaging device.

BACKGROUND OF THE INVENTION

Capturing images of light or other (including radiological) signalsemitted from specimens during a chemical reaction has been used todetermine the components of a specimen based on where spatiallyseparated bands or regions of light are emitted from the specimen.Certain components of a specimen may emit light in brighter bands oflight requiring shorter exposure times for image capture while otherconstituents may emit light in dimmer bands requiring longer exposuretimes. Problems can arise when “read noise” occurs during image captureand distorts the captured image, particularly for specimen componentsthat emit light in weakly emitting bands.

In order to overcome read noise limitations for weak samples, it iscommon to integrate or collect the charge over a long exposure of theCCD or CMOS. The long exposures do not allow the measurement system tomeasure the signal in continuous-like fashion. In other works, one couldtake many shorter images, but the system would not be very sensitivebecause read noise would be introduced with each short exposure. If yousum the short exposure, this helps reduce the read noise some but it isstill not as sensitive as conducting one long exposure using aconventional image sensor. In this case of image summing, the read noiseis known to increase in captured images as the square root of the numberof exposures.

Many trained artisans in the field have therefore struggled with solvingthe problem of monitoring weak chemical reactions in a continuous-likemanner while maintaining high sensitivity. As discuss below, there aseveral key advantages to method that would allow fast monitoring ofchemical reactions while not compromising sensitivity.

BRIEF SUMMARY OF THE INVENTION

Techniques for capturing images of a specimen in a chemical reactionusing a digital imaging device are described herein. At least certainembodiments are adapted to capture a series of short exposures of lightemissions from the specimen over a period of time using an array ofpixels of an image sensor in the digital imaging device. The images arecaptured by performing continuous non-destructive read operations toread out a set of non-destructive read images of the specimen from thepixel array. In one embodiment, images are captured by delaying the readout of the set of signals until at or near the end of the chemicalreaction to reduce read noise in the images.

The signals read out from the image sensor can be monitored and thecapturing of the images can be discontinued automatically or uponoccurrence of a predetermined event such as receiving a command from auser of the digital imaging device. The captured images can then bedisplayed in a graphical display.

One advantage of the techniques introduced herein is that almost no readnoise is introduced by capturing the series of short exposures using thenon-destructive read operations. These and other embodiments along withmany of their advantages and features are described in more detail inconjunction with the description below and attached figures.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A depicts a graphical representation of an image of a specimen ina chemiluminescence reaction captured using a series non-destructiveread operations according to one example embodiment;

FIG. 1B depicts a further graphical representation of an image of aspecimen in a chemiluminescence reaction captured using a seriesnon-destructive read operations according to one example embodiment;

FIG. 2 depicts an example block diagram of digital imaging device forcapturing an image of a specimen in a chemiluminescence reaction using aseries non-destructive read operations according to one embodiment;

FIG. 3A depicts an example flow chart of a process of capturing an imageof a specimen in a chemiluminescence reaction using a seriesnon-destructive read operations according to one embodiment;

FIG. 3B depicts an example flow chart of a process of using knownemission profile data to capture an image of a specimen in achemiluminescence reaction using a series non-destructive readoperations according to one embodiment;

FIG. 3C depicts an example flow chart of a process of using time-basedcurve fitting to capture an image of a specimen in a chemiluminescencereaction using a series non-destructive read operations according to oneembodiment;

FIG. 3D depicts an example flow chart of a process of using time profilemeasurements to discriminate light emitted from a specimen frombackground regions;

FIG. 4A depicts a plot of signal verses time for a reaction toillustrate the principles of non-destructive read operations and timeprofile according to exemplary embodiments.

FIG. 4B depicts a plot of signal verses time for a reaction toillustrate the principles of non-destructive read operations and timeprofile according to exemplary embodiments.

FIG. 4C depicts a plot of signal verses time for a reaction toillustrate the principles of non-destructive read operations and timeprofile according to exemplary embodiments.

FIG. 4D depicts a plot of signal verses time for a reaction toillustrate the principles of non-destructive read operations and timeprofile according to exemplary embodiments.

FIG. 4E depicts a plot of signal verses time for a reaction toillustrate the principles of non-destructive read operations and timeprofile according to exemplary embodiments.

FIG. 5 depicts an example block diagram of a data processing system uponwhich the disclosed embodiments may be implemented.

FIG. 6 depicts an exemplary device that can be used in embodiments ofthe invention.

DETAILED DESCRIPTION OF THE INVENTION

Throughout this description for the purposes of explanation, numerousspecific details are set forth in order to provide a thoroughunderstanding of the present invention. It will be apparent, however, toone skilled in the art that the present invention may be practicedwithout some of these specific details. In other instances, well-knownstructures and devices are shown in block diagram form to avoidobscuring the underlying principles of the described embodiments.

The methods and digital imaging devices introduced herein are adapted tocapture images of a specimen in a chemical reaction using a series ofshort exposures of light emissions from the specimen over a period oftime during a chemical reaction where the captured images growdynamically over the time period as the number of exposures increases.For example, in some embodiments, the specimen can be bound to ablotting membrane and the light emissions or other (e.g., radiological)signals are emitted directly or indirectly by a probe.

The series of short exposures is captured using an array of pixels of animage sensor in the digital imaging device configured for performingcontinuous non-destructive read operations. Non-destructive readoperations read out a set of electrical signals representingnon-destructive read images of the specimen from the pixel array. Theset of signals are generated from charge stored in the pixel array. Inone embodiment, images are captured by delaying the read out of the setof signals until at or near the end of the chemical reaction to reduceread noise in the images. Taking multiple images using non-destructiveread operations can reduce read noise so there is little penalty totaking multiple images and monitoring the signal in a continuous likemanner.

Embodiments are further configured to continuously monitor the signalsread out from the image sensor and to discontinue capturing images ofthe specimen upon a predetermined event such as receiving a command. Inone embodiment the commands can be generated automatically. In otherembodiments, the commands can be based on input from a user of thedigital imaging device. The captured images can then be displayed in agraphical display. Embodiments described herein are configured tocapture images of specimens in chemical reactions. The chemicalreactions can, for instance, include chemiluminescence reactions,fluorescence reactions, or absorbance reactions. Other types ofreactions are possible.

In a preferred embodiment, the digital imaging device is a complementarymetal-oxide-semiconductor (“CMOS”) digital imaging device capable ofperforming non-destructive read operations. CMOS digital imaging devicesexhibit minimal blooming due to over-saturation of bright pixels. Longexposures of bright bands of light emitted from the specimen can beperformed even if the bright bands are located in proximity to faintbands emitted from the specimen. But other digital imaging devices mayalso be used.

Further, the dynamic range of the captured images of the specimen can beincreased by combining data from shorter-time read images of the set ofnon-destructive read images for brighter areas of the specimen with datafrom longer-time read images of the set of non-destructive read imagesfor dimmer areas of the specimen. Combining the read data fromshorter-time non-destructive read images with read data from longer-timenon-destructive read images only requires data from a single measurementor non-destructive read exposure sequence.

Emission profiles of multiple different assays can also be obtained andstored in the memory of the digital imaging device. The emissionsprofiled include information relating to when an emission for aparticular specimen will begin rapidly declining. The emission profiledata is either known beforehand or can be measured by a user.

The emission profile data can be used to improve auto-exposure of theparticular specimen. Further, signals for bright bands can be determinedby expanding the bit depth of the captured digital image and calculatingthe signals for the bright bands based on a ratio of the exposure timeof the specimen taken by the digital imaging device to the totalexposure time obtained from emission profile data. The emission profiledata can also be used as a basis for querying the user of the digitalimaging device when an emission of a specimen is at or near its peak todetermine if the user wants to discontinue capturing images of thespecimen. Different weights can also be assigned to different frames ofthe series of non-destructive read images based on the emission profiledata.

In one embodiment, images of the specimen can be captured at a highframe rate using the non-destructive read operations and averaged at theend of the capture period to remove read noise. For instance, the framescan be captured only when intensity is stable enough based on theemission profile data. Each signal read out from the image sensor can beaveraged as a function of time to estimate the amount of signal presentto increase sensitivity of the image sensor. The intensity of eachsignal read out from the image sensor can then be calculated based onits location in the array of pixels in cases where the time profile ofthe signals is location dependent. The signals can then be shifted inlocation to the same time instance as if each of the signals startedsimultaneously at each location. This can be done to improverepeatability of the images captured by the digital imaging device.

Other embodiments are adapted to measure the time profile of the lightemitted from the specimen using the non-destructive read images as wellas the time profile of background regions close to one or more bands ofinterest in the captured image. The light emitted from the specimen canthen be discriminated from the background regions using a temporaldifference between the two time profiles. This can be done to improvesensitivity and repeatability of the image sensor and enable betterdiscrimination of any unwanted background noise from the signals readout from the image sensor.

In addition, black pixels in the background regions can be utilized tomeasure dark current noise. Dark current is the relatively smallelectric current that flows through photosensitive devices even when nophotons are entering the device. Dark current is one of the main sourcesfor noise in image sensors such as charge-coupled devices. Physically,dark current is due to the random generation of electrons and holeswithin the depletion region of the device that are then swept by thehigh electric field. The dark current noise can be measured dynamicallyfor each exposure and to eliminate local offsets and gain variationsarising from temperature variations based on the dark current noisemeasurements. The pattern of different dark currents can result in afixed-pattern noise. Fixed pattern dark noise reduction within thecaptured image can be improved based on the dark current noisemeasurements.

Imaging arrays are used to produce an image representing an object. Theimaging arrays are typically formed from rows and columns ofphotodetectors which generate photo-charges proportional to lightreflected from the object to be imaged. The photo-charges from eachpixel are converted to a signal (charge signal) or a potentialrepresentative of the level of energy reflected from a respectiveportion of the object and the signal or potential is read and processedby video processing circuitry to create the image. The output nodes ofpixels in the same column are usually commonly connected and each pixelin the column is individually controlled to read-out at the commonoutput node.

In non-destructive reads, the light information is continuously storedin the imaging device even during the read out process. FIG. 1A depictsa graphical representation of an image of a specimen in achemiluminescence reaction captured using a series non-destructive readoperations according to one example embodiment. Chemiluminescence is theemission of light (luminescence), as the result of a chemical reaction.There may also be limited emission of heat. Chemiluminescence differsfrom fluorescence in that the electronic excited state is derived fromthe product of a chemical reaction rather than the more typical way ofcreating electronic excited states, namely absorption. It is theantithesis of a photochemical reaction, in which light is used to drivean endothermic chemical reaction. In chemiluminescence, light isgenerated from a chemically exothermic reaction.

In the illustrated embodiment, the image captured grows dynamically ateach time increment 101, 102, and 103 as the number of exposuresincreases over the image capture time period. As can be seen, the imagescaptured of the bright bands shows significant detail while the faintbands are still growing. FIG. 1B depicts a further graphicalrepresentation of an image of a specimen in a chemiluminescence reactioncaptured using a series non-destructive read operations. In thisdepiction, the distortion on the brighter bands from read noise worsenswith each time increment 104, 105 and 106 as the number of exposuresincreases over the image capture time period. But at these later times,the detail of the images of the faint bands has increased from theearlier images. This leads to problems in capturing high-quality imagesfor components that emit light in dimmer bands of a specimen in achemical reaction while minimizing the distortion for images ofcomponents that emit light in brighter bands.

FIG. 2 depicts an example block diagram of digital imaging device forcapturing an image of a specimen in a chemiluminescence reaction using aseries non-destructive read operations according to one embodiment. Inthe illustrated embodiment, digital imaging device 200 includes aprocessor 201 and a system memory 204 coupled together via data bus 215.For the purposes of the present disclosure, processor 201 can be anyprocessor known in the art including a microprocessor or microcontrollerof any sort that is capable of executing instructions to performoperations. Likewise, system memory 204 can be any type of memory knownin the art that is capable of storing data (220) and instructions (222)such as a random access memory (RAM), read-only memory (ROM), or othervolatile or nonvolatile memories, etc.

Digital imaging device 200 further includes an image sensor 202 coupledwith data bus 215. An image sensor is a device that converts an opticalimage into an electronic signal. It is used mostly in digital cameras,camera modules and other imaging devices. Most currently used imagesensors are digital charge-coupled devices (“CCDs”) or complementarymetal-oxide-semiconductor (“CMOS”) active pixel sensors. Image sensor202 includes an array of pixels for capturing a series of shortexposures of light emissions from a specimen over a period of timeduring a chemical reaction. Image sensor 202 can be configured toperform continuous non-destructive read operations to read out a set ofsignals representing non-destructive read images of the specimen fromthe array of pixels by delaying the reading out the signals until theend of the time period to reduce read noise in the set ofnon-destructive read image signals.

Digital imaging device 200 further includes a monitoring module 210coupled with the data bus 215. Monitoring module 210 can be configuredin certain embodiments to continuously monitor signals read out from theimage sensor and discontinue capturing images of the specimen eitherautomatically or based on input from a user of the digital imagingdevice. Digital imaging device 200 further includes a graphical displaydevice 203 to display the captured images of the specimen.

FIG. 3A depicts an example flow chart of a process of capturing an imageof a specimen in a chemiluminescence reaction using a seriesnon-destructive read operations according to one embodiment. In theillustrated embodiment, process 300A begins at operation 301 where aseries of short exposures of light emissions from the specimen iscaptured over a period of time during the reaction using a series ofnon-destructive read operations to read out a set of signalsrepresenting non-destructive read images of the specimen from the arrayof pixels of the image sensor. In one embodiment, the reading out of theset of signals is delayed until the end of the time period to reduceread noise in the set of non-destructive read images.

Process 300A continues by continuously monitoring the set of signalsread out from the image sensor (operation 302) and discontinuingcapturing images of the specimen upon occurrence of a predeterminedevent (operation 303). In one embodiment, the image capture can bediscontinued automatically. In other embodiments, the predeterminedevent includes receiving a command from a user of the digital imagingdevice. Other predetermined events are possible.

The dynamic range of the captured images of the specimen can then beincreased by combining data from shorter-time read images for brighterareas of the specimen with data from longer-time read images for dimmerareas of the specimen (operation 304). The captured images of thespecimen can then be displayed in a graphical display (operation 305).This completes process 300A according to one example embodiment.

FIG. 3B depicts an example flow chart of a process of using knownemission profile data to capture an image of a specimen in achemiluminescence reaction using a series non-destructive readoperations according to one embodiment. In the illustrated embodiment,process 300B begins at operation 310 by storing in memory of the digitaldevice emission profile data of multiple different assays includinginformation relating to when an emission for a particular assay willbegin rapidly declining. The emission profile data can either be knownbeforehand or measured by a user of the digital imaging device.

In one embodiment, the emission profile data is used to improveauto-exposure of the particular specimen at operation 311. Process 300Bcontinues at operation 312 by querying the user of the digital imagingdevice when an emission of a specimen is at or near its peak based onthe emission profile data to ask the user whether to discontinuecapturing images of the specimen. Process 300B further includesoperation 313 where a signal for one or more bright bands of emissionsfrom the specimen is calculated based on the ratio of the period of timeof exposure taken by the digital imaging device to the total time of theexposure of emissions obtained from the emission profile data. Differentweights are assigned to different frames of the series ofnon-destructive read images based on the emission profile data Thiscompletes process 300B according to one example embodiment.

FIG. 3C depicts an example flow chart of a process of using time-basedcurve fitting to capture an image of a specimen in a chemiluminescencereaction using a series non-destructive read operations according to oneembodiment. In the illustrated embodiment, process 300C begins atoperation 321 by calculating the intensity of each signal read out fromthe image sensor based on location of the signal in the array of pixelsin cases where the time profile of each signal is location dependent.Each signal is then averaged as a function of time to estimate an amountof signal present (operation 322) and the locations of the averagedsignals are shifted in time to the same time instance as if each of thesignals at each location started simultaneously. In one embodiment, thisis done to improve repeatability of the image capture operation. Thiscompletes operation 300C according to one example embodiment.

FIG. 3D depicts an example flow chart of a process of using time profilemeasurements to discriminate light emitted from a specimen frombackground regions according to one embodiment. In the illustratedembodiment, process 300D begins at operation 330 by measuring the timeprofile of the light emitted from the specimen using the non-destructiveread images. Operation 300D continues by measuring the time profile of abackground region in proximity to one or more bands of interest in thecaptured images (operation 331) and discriminating the light emittedfrom the specimen from the background region using the temporaldifference between the measured time profiles to discriminate thesignals read out from the image sensor from unwanted background noise(operation 332).

It should be appreciated that the specific operations illustrated inFIGS. 3A-3D provide a particular method of capturing an image of aspecimen in a chemiluminescence reaction using a series ofnon-destructive read operations according to one embodiment. Othersequences of operations may also be performed according to alternativeembodiments. For example, alternative embodiments may perform theoperations outlined above in a different order and additional operationsmay be added or removed depending on the particular applications.Moreover, the individual operations may include one or moresub-operations that may be performed in various sequences asappropriate.

FIGS. 4A-4D depict plots of signal intensity verses time forchemiluminescence reactions to illustrate the principles ofnon-destructive read operations and time profile according to exemplaryembodiments. In the illustrated embodiment of FIG. 4A, the signal isintegrated only between time instances t1 and t2 for best results.Between times t1 and t2, the signal intensity is strong enough and yetstill far enough away from the start of the reaction. Times t1 and t2can be determined retroactively by analyzing the data that was capturedusing non-destructive read mode (i.e., taking a series of images). Timest1 and t2 can be determined by the user before or after the experiment.Time t1 can also be zero. An automated algorithm can be used todetermine when times t1 and t2 occur, for example by the followingmethods: (1) when the time-based derivative of the signal reaches apredetermined threshold; or (2) by fitting the time curve to a knownmodel that has predetermined t1 and t2 that are related to parameters inthe model such as a time delay parameter, amplitude of the curve etc.

In the illustrated embodiment of FIG. 4B, the signal intensity isintegrated only between times t1 and t2 for best results. As can be seenin this case, between times t1 and t2 the signal intensity is higherthan the rest of the time curve. Times t1 and t2 can be determinedretroactively by analyzing the data that was captured usingnon-destructive read mode (i.e., taking a series of images). Times t1and t2 can be determined by the user before or after the experiment.Time t1 can also be zero. An automated algorithm can be used todetermine when times t1 and t2 occur, for example by the followingmethods: (1) when the absolute value of the time-based derivative of thesignal is smaller than a predetermined threshold, but is near the peakof the curve where the derivative is approximately zero; or (2) byfitting the time curve to a known model that has predetermined t1 and t2that are related to parameters in the model such as a time delayparameter, amplitude of curve, etc.

In the illustrated embodiment of FIG. 4C, the signal intensity isintegrated only between times t1 and t2 for best results. As can be seenin this case, between times t1 and t2 the signal intensity isapproximately constant. Times t1 and t2 can be determined retroactivelyby analyzing the data that was captured using non-destructive read mode(i.e., taking a series of images). Times t1 and t2 can be determined bythe user before or after the experiment. Time t1 can also be zero. Anautomated algorithm can be used to determine when times t1 and t2 occur,for example by the following methods: (1) when the signal derivativewith time is small enough after being large and positive for time valuesof t<t1, and before being large and negative after time values t>t2using some threshold; (2) when the signal derivative with time issmaller than some threshold; (3) by fitting the curve to a known modelthat has predetermined t1 and t2 that are related to parameters in themodel such as a time delay parameter, amplitude of the curve, etc.; or(4) the entire signal is integrated numerically, but only the linearpart of the integral between t1 and t2 is taken into account (theintegral is approximately linear where the curve is approximatelyconstant). Deviation from linearity is determined by thresholds (such asR-squared smaller than some value) or distance of points from a linearfit.

In the illustrated embodiment of FIG. 4D, if for some reason the signalat different bands or areas has a delay in time because of such thingsas user operations, temperature variations, fluid arrival delay,experiments preformed at different times, or different instruments, thenthe integration of the signal between predetermined times such asdescribed will reduce signal variation and improve repeatability. Thisis because with current techniques, only the final integral (sum) of thesignal is known. Therefore time delays are not noticeable by themeasurement system or user.

In the illustrated embodiment of FIG. 4E, if the time profile of thesignal generated at a background area (because of non-specific bindingfor example) is different from that of the target signal, then byfinding deviations from the known or measured model of the time profileand excluding those unwanted signals can improve SNR and repeatability.Deviation from the model can be found, for example, by setting athreshold on CHI square of a nonlinear curve fit of these curves. Withcurrent techniques only the final integral (sum) of the signal is known.Therefore different signal profiles are not noticeable by themeasurement system or user, and therefore cannot be excluded as here.

In some embodiments, the specimen is a biological sample, e.g., aprotein or nucleic acid (e.g., DNA, RNA, or both) sample. The sample canbe bound to a blotting membrane and images of the blotting membranes aredetermined. Blotting techniques are commonly used in biochemicalanalyses. For example, mixed samples of biological entities are directlyapplied to a membrane (e.g., “dot blotting”) or applied toelectrophoretic gels and the components are separated by application ofan electric field across the gel and then applied to a membrane (e.g.,Southern, northern, or western blotting). The resulting pattern ofmigration of the substances contained in the sample is then detected insome manner. Biochemical targets (e.g., a target nucleic acid orprotein) are then detected by a probe that binds to the target(s).Exemplary probes include antibodies, other non-antibody proteins, ornucleic acids. In some cases (e.g., when the probe is not directlylabeled), the membrane is then treated and incubated with a secondaryenzyme-, radioisotope-, fluorfluor-, or biotin- or otherlabel-conjugated antibody specific for the primary probe.

Optionally, a detector reagent, e.g., a chromogenic, chemiluminescent,fluorescent, radiological, or streptavidin-labeled material, is appliedwhich either binds to, or is a substrate of an enzyme linked to theprobe, thereby generating a signal. It will be appreciated that there isa wide variety of ways signal from the probe is ultimately generated.Basic texts disclosing the general methods of various blottingtechniques include Sambrook and Russell, Molecular Cloning, A LaboratoryManual (3rd ed. 2001); Kriegler, Gene Transfer and Expression: ALaboratory Manual (1990); and Current Protocols in Molecular Biology(Ausubel et al., eds., 1994-1999).

In general however, the non-destructive read-out techniques describedherein can be applied to various other fields to increase dynamic rangeand signal-to-noise ratio. For example, slowly changing microscopyobjects, (relative to the frame rate) such as cells, could be visualizedbetter using non-destructive read-out operations by averaging manyframes (reducing read noise) and increased dynamic range. Plate readersare another example where non-destructive read-out operations can beperformed. Further, the cost of many imaging systems that usecharge-coupled device (“CCD”) image sensors can be reduced by going toCMOS digital imaging devices. The loss in sensitivity of such CMOSdevices as compared to CCD devices can be regained by using anon-destructive read-out mode. The non-destructive read-out techniquesdescribed herein could also be used in contact imaging microscopy, whichis a developing field in the last few years. Other examples of processesthat can be used with the techniques described herein are included inExhibit A.

FIG. 5 depicts an example block diagram of a data processing system uponwhich the disclosed embodiments may be implemented. Embodiments of thepresent invention may be practiced with various computer systemconfigurations such as hand-held devices, microprocessor systems,microprocessor-based or programmable user electronics, minicomputers,mainframe computers and the like. The embodiments can also be practicedin distributed computing environments where tasks are performed byremote processing devices that are linked through a wire-based orwireless network. FIG. 5 shows one example of a data processing system,such as data processing system 500, which may be used with the presentdescribed embodiments. Note that while FIG. 5 illustrates variouscomponents of a data processing system, it is not intended to representany particular architecture or manner of interconnecting the componentsas such details are not germane to the techniques described herein. Itwill also be appreciated that network computers and other dataprocessing systems which have fewer components or perhaps morecomponents may also be used. The data processing system of FIG. 5 may,for example, a personal computer (PC), workstation, tablet, smartphoneor other hand-held wireless device, or any device having similarfunctionality.

As shown, the data processing system 501 includes a system bus 502 whichis coupled to a microprocessor 503, a Read-Only Memory (ROM) 507, avolatile Random Access Memory (RAM) 505, as well as other nonvolatilememory 506. In the illustrated embodiment, microprocessor 503 is coupledto cache memory 504. System bus 502 can be adapted to interconnect thesevarious components together and also interconnect components 503, 507,505, and 506 to a display controller and display device 508, and toperipheral devices such as input/output (“I/O”) devices 510. Types ofI/O devices can include keyboards, modems, network interfaces, printers,scanners, video cameras, or other devices well known in the art.Typically, I/O devices 510 are coupled to the system bus 502 through I/Ocontrollers 509. In one embodiment the I/O controller 509 includes aUniversal Serial Bus (“USB”) adapter for controlling USB peripherals orother type of bus adapter.

RAM 505 can be implemented as dynamic RAM (“DRAM”) which requires powercontinually in order to refresh or maintain the data in the memory. Theother nonvolatile memory 506 can be a magnetic hard drive, magneticoptical drive, optical drive, DVD RAM, or other type of memory systemthat maintains data after power is removed from the system. While FIG. 5shows that nonvolatile memory 506 as a local device coupled with therest of the components in the data processing system, it will beappreciated by skilled artisans that the described techniques may use anonvolatile memory remote from the system, such as a network storagedevice coupled with the data processing system through a networkinterface such as a modem or Ethernet interface (not shown).

FIG. 6 shows an exemplary device 1000 that can be used in embodiments ofthe invention. The device 1000 may be an imaging device. It isunderstood that this is an exemplary device and that many other devicesmay be used with embodiments of the invention (e.g., cameras, x-raymachines, etc.). The device 1000 may be used to capture images of lightemitted from specimens placed on the device. For example, the device1000 may comprise a body 1001, a display 1003 (e.g., a touch screen,etc.), and a lid 1005 that rests over a surface area such as a faceplate(e.g., a fiber faceplate) for placing one or more specimens on thedevice 1000. The faceplate may protect the sensor from a sample orspecimen placed on the faceplate. The faceplate may be lightproof,waterproof and easy to clean. A user may lift the lid 1005, place thespecimen on the faceplate of the device 1000, and close the lid 1005.The device 1000 may begin to capture images automatically or in responseto an indication from the user, such as pushing a button on the display1003.

As explained above, in some embodiments, the specimen is a biologicalsample, e.g., a protein or nucleic acid (e.g., DNA, RNA, or both)sample. The sample can be bound to a blotting membrane and images of theblotting membranes comprising labeled probes can be determined. Blottingtechniques are commonly used in biochemical analyses. For example, mixedsamples of biological entities are directly applied to a membrane (e.g.,“dot blotting”) or applied to electrophoretic gels and the componentsare separated by application of an electric field across the gel andthen applied to a membrane (e.g., Southern, northern, or westernblotting). The resulting pattern of migration of the substancescontained in the sample is then detected in some manner. Biochemicaltargets (e.g., a target nucleic acid or protein) are then detected by aprobe that binds to the target(s). Exemplary probes include antibodies,other non-antibody proteins, or nucleic acids. In some cases (e.g., whenthe probe is not directly labeled), the membrane is then treated andincubated with a secondary enzyme-, radioisotope-, fluorfluor-, orbiotin- or other label-conjugated antibody specific for the primaryprobe.

Optionally, a detector reagent, e.g., a chromogenic, chemiluminescent,fluorescent, radiological, or streptavidin-labeled material, is appliedwhich either binds to, or is a substrate of an enzyme linked to theprobe, thereby generating a signal. It will be appreciated that there isa wide variety of ways signal from the probe is ultimately generated.Basic texts disclosing the general methods of various blottingtechniques include Sambrook and Russell, Molecular Cloning, A LaboratoryManual (3rd ed. 2001); Kriegler, Gene Transfer and Expression: ALaboratory Manual (1990); and Current Protocols in Molecular Biology(Ausubel et al., eds., 1994-1999).

The device 1000 may further comprise an internal power supply and inputand output jacks for various components (e.g., a printer, an externalcomputer, an external display, external power supply, etc.). The inputand output jacks may be wired or wireless according to known techniquesand devices.

The device 1000 may further comprise a sensor (e.g., an image sensor).There are various types of sensors that may be utilized in embodimentsof the invention. Some examples of sensor technology include chargecoupled device (CCD) or complementary metal oxide semiconductor (CMOS)sensors (e.g., 11×6.9 cm active area, 8.7×13.9 cm, 10.4×15.6 cm, etc.).The sensor may be directly coupled with the faceplate on the device ormay be coupled with an imaging system and the imaging system may becoupled with the faceplate. The sensor may comprise an array of pixels.In embodiments of the invention the array of pixels may be atwo-dimensional array or a linear or one-dimensional array.

The device may further comprise a processor coupled with the sensor. Theprocessor of the device may be configured to perform various processesassociated with the device. For example, the processor may be configuredto capture a series of short exposures of light emissions from thespecimen over a period of time during the reaction, wherein capturedimages of the specimen grow dynamically over the period of time as thenumber of exposures increases, wherein the series of short exposures iscaptured using an array of pixels of an image sensor of a digitalimaging device configured to perform continuous non-destructive readoperations to read out a set of signals representing non-destructiveread images of the specimen from the array of pixels of the imagesensor, and wherein reading out the set of signals is delayed until theend of the period of time to reduce read noise in the set ofnon-destructive read images, monitor the set of signals read out fromthe image sensor, and discontinue capturing images of the specimen uponreceiving a command, wherein the command is generated automatically oris based on input from a user of the digital imaging device.

With these embodiments in mind, it will be apparent from thisdescription that aspects of the described techniques may be embodied, atleast in part, in software, hardware, firmware, or any combinationthereof. It should also be understood that embodiments can employvarious computer-implemented functions involving data stored in a dataprocessing system. That is, the techniques may be carried out in acomputer or other data processing system in response executing sequencesof instructions stored in memory. In various embodiments, hardwiredcircuitry may be used independently, or in combination with softwareinstructions, to implement these techniques. For instance, the describedfunctionality may be performed by specific hardware componentscontaining hardwired logic for performing operations, or by anycombination of custom hardware components and programmed computercomponents. The techniques described herein are not limited to anyspecific combination of hardware circuitry and software.

Embodiments herein may also be in the form of computer code stored on acomputer-readable medium. Computer-readable media can also be adapted tostore computer instructions, which when executed by a computer or otherdata processing system, such as data processing system 500, are adaptedto cause the system to perform operations according to the techniquesdescribed herein. Computer-readable media can include any mechanism thatstores information in a form accessible by a data processing device suchas a computer, network device, tablet, smartphone, or any device havingsimilar functionality. Examples of computer-readable media include anytype of tangible article of manufacture capable of storing informationthereon such as a hard drive, floppy disk, DVD, CD-ROM, magnetic-opticaldisk, ROM, RAM, EPROM, EEPROM, flash memory and equivalents thereto, amagnetic or optical card, or any type of media suitable for storingelectronic data. Computer-readable media can also be distributed over anetwork-coupled computer system, which can be stored or executed in adistributed fashion.

Throughout the foregoing description, for the purposes of explanation,numerous specific details were set forth in order to provide a thoroughunderstanding of the invention. It will be apparent, however, to personsskilled in the art that these embodiments may be practiced without someof these specific details. Accordingly, the scope and spirit of theinvention should be judged in terms of the claims which follow as wellas the legal equivalents thereof.

What is claimed is:
 1. A method of capturing digital images of aspecimen in a chemical reaction comprising: capturing, by an imagingdevice, a series of short exposures of light emissions from the specimenover a period of time during the reaction, wherein captured images ofthe specimen grow dynamically over the period of time as the number ofexposures increases, wherein the series of short exposures is capturedusing an array of pixels of an image sensor of a digital imaging deviceconfigured to perform continuous non-destructive read operations to readout a set of signals representing non-destructive read images of thespecimen from the array of pixels of the image sensor, and whereinreading out the final set of signals is delayed until the end of theperiod of time to reduce read noise in the set of non-destructive readimages; monitoring, by the imaging device, the sets of signalsrepresenting the non-destructive read images read out from the imagesensor; discontinuing capturing images of the specimen, by the imagingdevice, upon receiving a command, wherein the command is generated basedon the monitored signals; and increasing a dynamic range of the capturedimages of the specimen by combining data from shorter-time read imagesof the set of non-destructive read images for brighter areas of thespecimen with data from longer-time read images of the set ofnon-destructive read images for dimmer areas of the specimen.
 2. Themethod of claim 1 further comprising displaying the captured images ofthe specimen in a graphical display.
 3. The method of claim 1 whereinthe digital imaging device comprises a complementarymetal-oxide-semiconductor (“CMOS”) digital imaging device capable ofperforming non-destructive read operations.
 4. The method of claim 3wherein images captured using the CMOS digital imaging device exhibitminimal blooming due to over-saturation from bright pixels, and whereinlong exposures of bright bands of light emitted from the specimen areperformed even if the bright bands are located in proximity to faintbands emitted from the specimen.
 5. The method of claim 1 furthercomprising: storing in a memory of the digital imaging device emissionprofile data of multiple different assays including information relatingto when an emission for a particular assay will begin rapidly declining;and selecting the end of the period of time based at least in part onthe emission profile of the particular assay.
 6. The method of claim 5further comprising: expanding bit depth of the captured images; andcalculating a signal for one or more bright bands of emissions from thespecimen based on a ratio of the period of time of exposure of emissionsfrom the specimen taken by the digital imaging device to a total time ofthe exposure of emissions from the specimen obtained from the emissionprofile data.
 7. The method of claim 5 wherein the emission profile datais either known beforehand or measured by a user of the digital imagingdevice.
 8. The method of claim 5 further comprising using the emissionprofile data to improve auto-exposure of the particular specimen.
 9. Themethod of claim 5 further comprising querying the user of the digitalimaging device when an emission of a specimen is at or near its peakbased on the emission profile data to ask the user whether todiscontinue capturing images of the specimen.
 10. The method of claim 5wherein different weights are assigned to different frames of the seriesof non-destructive read images based on the emission profile data. 11.The method of claim 1, further comprising: capturing images of thespecimen at a high frame rate using the non-destructive read operations;and averaging frames captured at the end of the period of time to reduceread noise.
 12. The method of claim 1 further comprising averaging orapplying curve fitting methods of each signal read out from the imagesensor as a function of time to estimate an amount of signal present toincrease sensitivity of the image sensor in the digital imaging device.13. The method of claim 1 further comprising: calculating an intensityof each signal read out from the image sensor based on location of thesignal in the array of pixels, wherein a time profile of each signal islocation dependent; averaging each signal as a function of time toestimate an amount of signal present; and shifting locations of theaveraged signals to a same time instance as if each of the signals ateach location started simultaneously.
 14. The method of claim 1 whereinthe reaction is a chemiluminescence reaction, a fluorescence reaction,or an absorbance reaction.
 15. The method of claim 1 further comprising:measuring a first time profile of the light emitted from the specimenusing the non-destructive read images; measuring a second time profileof a background region close to one or more bands of interest in thecaptured images; and discriminating the light emitted from the specimenfrom the background of the images using a temporal difference betweenthe first and second time profiles to discriminate the signals read outfrom the image sensor from unwanted background noise.
 16. The method ofclaim 1 further comprising: utilizing black pixels in a backgroundregion in proximity to a band of interest in the captured images tomeasure dark current noise for each exposure; and eliminating localoffsets and gain variations arising from temperature variations based onthe dark current noise measurements.
 17. The method of claim 16 furthercomprising improving fixed pattern dark noise reduction within thecaptured images based on the dark current noise measurements.
 18. Adigital imaging device for capturing digital images of a specimen in achemical reaction comprising: a processor; a memory coupled with theprocessor via an interconnect bus; an image sensor comprising an arrayof pixels for capturing a series of short exposures of light emissionsfrom the specimen over a period of time during the reaction, whereincaptured images of the specimen grow dynamically over the period of timeas the number of exposures increases, wherein the image sensor isconfigured to perform continuous non-destructive read operations to readout a set of signals representing non-destructive read images of thespecimen from the array of pixels, and wherein the final reading out thesignals is delayed until the end of the period of time to reduce readnoise in the set of non-destructive read images; and a monitoring moduleconfigured to continuously monitor the signals representing thenon-destructive read images read out from the image sensor anddiscontinue capturing images of the specimen based on the monitoredsignals; wherein the digital imaging device is further configured toincrease a dynamic range of the captured images of the specimen bycombining data from shorter-time read images of the set ofnon-destructive read images for brighter areas of the specimen with datafrom longer-time read images of the set of non-destructive read imagesfor dimmer areas of the specimen.
 19. The digital imaging device ofclaim 18 further comprising a graphical display configured to displaythe captured images of the specimen.